Next Generation Sequencing Facilitates Quantitative Analysis of NP1 and NP1/CRTCHA Gut Transcriptomes
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ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE185159 | GEO | 2022/08/10
REPOSITORIES: GEO
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Project description:Purpose: The goals of this study are to compare the transcriptome of Arabidopsis seedlings expressing pTaF5H1:TaF5H1(expression of TaF5H1 driven by its native promoter) with the wild-type control(Col-0) under/without salt treatment, which may give us clues to whether and how cell wall composition changes affect salt tolerance. Transcriptomes profiles of 14-day-old Arabidopsis seedlings of wild-type (Col-0) and seedlings harbour pTaF5H1:TaF5H1 without and under NaCl treatment for 6 hours were generated by RNA-seq, in triplicate, using Illumina a HiSeq instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA). Sequencing was carried out using a 2x150 paired-end (PE) configuration; image analysis and base calling was conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument. In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format was processed by Cutadapt (V1.9.1) to be high quality clean data. For mapping, firstly, reference genome sequences and gene model annotation files of relative species were downloaded from ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1). For expression analysis, in the beginning, transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data. For differential expression analysis, DESeq2 Bioconductor package was used, a model based on the negative binomial distribution, the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones. Results: we mapped about 43.5 million sequence reads per sample to the Arabidopsis genome (TAIR10). Significant differential expressed genes(DEG) between samples was sreened for fold change≥2 and p-value (fdr, padj)≤0.05.Totally 7713 significant DEGs were discovered with 3430 up -regulated and 4483 down-regulated, no significant changes were detected as for the remaining 26505 genes among samples. Conclusions: Our study presents the detailed analysis of transcriptomes of Arabidopsis wild-type control(Col-0) and Arabidopsis seedlings expressing pTaF5H1:TaF5H1, with three biologic replicates, generated by RNA-seq technology. Our results show that ectopic expressing pTaF5H1:TaF5H1 in Arabidopsis changed the expression of some cell-wall related genes as well as genes related to salt stress response, inferring that changes in cell wall components may affect the salt tolerance of plants somehow.
2022-03-25 | GSE199116 | GEO
Project description:CREB-Regulated Transcription Co-activator (CRTC) regulates metabolism in liver where activation by calcineurin regulates gluconeogenic genes. CaN also has roles in pathological cardiac hypertrophy, however cardiac roles for CRTC have not been identified. In Drosophila, CRTC null mutants exhibit severe cardiac restriction, myofibrillar disorganization, cardiac fibrosis, and tachycardia. Cardiac-specific knockdown (KD) of CRTC mimicked the heart defects of CRTC mutants and cardiac-overexpression (OE) of CRTC or calcineurin caused hypertrophy that was reduced in CRTC mutants, suggesting CRTC mediates calcineurin’s effects. RNAseq of CRTC KD or OE hearts revealed contra-regulated genes involved in glucose, fatty acid, and amino acid metabolism. Genes with conserved CREB binding sites included the fly ortholog of Sarcalumenin, a Ca2+-binding protein. Cardiac KD of this gene recapitulated CRTC KD restriction and fibrotic phenotypes. KD in zebrafish also caused restriction, indicating a conserved role in cardiomyocyte maintenance, and suggesting CaN-CRTC-Sarcalumenin signaling represents a novel pathway underlying cardiac hypertrophy.
2024-07-29 | GSE271481 | GEO
Project description:Purpose: We tested global gene transcriptome changes by RNA-sequencing analysis in the offspring breast tumors of SV40 transgenic mice to further identify key epigenetic-controlled genes in regulation of the prenatal/maternal BSp diet-mediated early breast cancer prevention. Method: Mouse offspring mammary tumor mRNA from control and maternal BSp treatment were generated by deep sequencing, in duplicate or triplicate, using Illumina NextSeq500 platform (GPL19057). The sequence reads that passed quality filters were analyzed. We utilized the R/Bioconductor package DESeq to evaluate differential gene expression for sequence count data by the use of negative binomial distributio. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Conclusions: Our data showed differential transcriptome distribution in the breast tumors of mouse offspring between the control and prenatal/maternal BSp treatment groups.
2018-05-02 | GSE113900 | GEO
Project description:Purpose: Exploring the alteration in CREB/CRTC binding related to long-term memory Methods: The nuclei of Drosophila mushroom bodies were purified and the histone acetylation and CREB/CRTC binding were examined by ChIP-seq using specific antibodies. The sequencing was performed using Miseq, and aligned to dm3 using CLCbio. The sequence reads that passed quality filters were analyzed by peak calling using PICS and ERD equipped on Strand NGS software. This method using two algorisms excludes false-positive calling of peaks. The PICS and ERD were run using a default setting except for the following parameters; for PICS, 120 bp as an average fragment length, 10 bp as a minimum distance between forward and reverse reads, 200 bp as a minimum distance between forward and reverse reads, 100 bp as a window width, with 5% false discovery rate; for ERD, 1.5 as an enrichment factor, 100 bp as a window size, 10 bp as a window slide size, 100 bp as a minimum region size. The peaks obtained by ERD analysis were filtered by an enrichment factor of 2, and a density of reads at 0.12 for CREB and 0.2 for CRTC. The CREB and the CRTC binding sites were determined as the peak-called region in at least 2 samples out of the three replicates. The CREB and the CRTC binding sites located 200 bp vicinity to each other were defined as the CREB/CRTC binding sites. In parallel, the read counts were obtained in the 1 kb window covering entire genome and analyzed by DESeq2, to determine the region enriched with CREB/CRTC in a specific group of samples. The region with increased or decreased CREB/CRTC binding were determined if the region were defined by the CREB/CRTC binding sites in the above criteria. Results: Using an optimized data analysis workflow, the filtered reads amounted to 8-11million reads for CREB in each of 3 replicates, 8-17 million reads for CRTC in each of 3 replicates, and 4.4 million reads for input. Using anti-CREB antibody, we found 239 significant increases in CREB binding out of 4995 CREB/CRTC binding sites 1 day after training. Using anti-CRTC antibody, we found 4989 significant increases in CRTC binding out of 4995 CREB/CRTC binding sites 1 day after spaced training. Conclusions: Our study shows that, although CREB binding is mostly unchanged, CRTC binding is significantly increased after long-term memory formation in Drosophila mushroom bodies.
2017-02-09 | GSE81456 | GEO
Project description:We profiled the transcriptome of Dexamethasone-, Tofacitinib-, Tacrolimus-, Prednisolone-, sodium lauryl sulfate (SLS)-, Aciclovir-, Benzoic acid-, Genistein-, Ribavirin-, Mercuric chloride-, Cyclosporine- and LPS-treated monocytes and without chemical-treated (basal, vehicle) monocytes. A Bioconductor software package in R called edgeR was used to conduct the differential expression analysis. Lowly expressed genes were filtered out by keeping only genes with worthwhile counts in a minimum number of samples. The default normalization method in edgeR, trimmed mean of M-values (TMM) normalization was performed, and dispersion estimates (common and tagwise dispersions) were obtained to proceed with differential expression determination. Differentially expressed genes were determined by conducting pairwise comparisons between each type of immunosuppressor or non-immunosuppressor and vehicle or control by applying fold-change and p-value cutoffs (|fold-change| > 1.5 and p-value < 0.05). Each immunosuppressor, excluding sodium lauryl sulfate, was compared with the vehicle group. Immunosuppressor sodium lauryl sulfate and non-immunosuppressor lipopolysaccharide were compared with the basal group. Non-immunosuppressors genistein and ribavirin were compared with the vehicle group.
2021-12-11 | GSE190511 | GEO
Project description:Low energy states delay aging in multiple species, yet mechanisms coordinating energetics and longevity across tissues remain poorly defined. The conserved energy sensor AMP-activated protein kinase (AMPK) and its corresponding phosphatase calcineurin modulate longevity via the ‘CREB regulated transcriptional coactivator (CRTC)-1 in C. elegans. We show that CRTC-1 specifically uncouples AMPK/calcineurin mediated effects on lifespan from pleiotropic side effects by reprogramming mitochondrial and metabolic function. Strikingly, this pro-longevity metabolic state is regulated cell-nonautonomously by CRTC-1 in the nervous system. CRTC-1/CREB act antagonistically with the functional PPARα ortholog, NHR-49 to promote distinct peripheral metabolic programs. Neuronal CRTC-1 drives mitochondrial fragmentation in distal tissues and suppresses the effect of AMPK on systemic mitochondrial metabolism and longevity via a cell-nonautonomous catecholamine signal. These results demonstrate that transcriptional control of neuronal signals can override enzymatic regulation of metabolism in peripheral tissues. Central perception of energetic state therefore represents a target to promote healthy aging.
2015-02-27 | GSE58931 | GEO
Project description:Purpose: to identify how condensin I removal affects gene expression globally. Methods: Chicken DT40 CAP-H KO cells were treated with or without dox for 36 h. Total RNA samples were extracted and subjected to sequencing using an Illumina Hiseq2000 platform. Library preparation and Illumina sequencing were performed by Macrogen (South Korea). The sequence tags were spliced-mapped onto the chicken genome galGal4 using Tophat and Bowtie2 following quality test using FASTQC. Differential expression of genes was analyzed using the Bioconductor v2.3 package edgeR v3.2.3. Tag enrichment in NCBI RefSeq genes was calculated between dox-treated and untreated cells using edgeR exact test with tag-wise dispersion estimation. Results: We identified a total of 3798 genes to be differentially expressed in G1 condensin I-depleted chicken DT40 cells: 2495 down regulated and 1303 up regulated. Conclusions: Removal of CAP-H leads to significant misregulation of gene expression, suggesting a key role for condensin I in transcription during interphase.
2017-05-03 | GSE74892 | GEO
Project description:Purpose: to identify how condensin I removal affects gene expression globally. Methods: Chicken DT40 CAP-H KO cells were treated with or without dox for 36 h. Total RNA samples were extracted and subjected to sequencing using an Illumina Hiseq2000 platform. Library preparation and Illumina sequencing were performed by Macrogen (South Korea). The sequence tags were spliced-mapped onto the chicken genome galGal4 using Tophat and Bowtie2 following quality test using FASTQC. Differential expression of genes was analyzed using the Bioconductor v2.3 package edgeR v3.2.3. Tag enrichment in NCBI RefSeq genes was calculated between dox-treated and untreated cells using edgeR exact test with tag-wise dispersion estimation. Results: We identified a total of 3798 genes to be differentially expressed in G1 condensin I-depleted chicken DT40 cells: 2495 down regulated and 1303 up regulated. Conclusions: Removal of CAP-H leads to significant misregulation of gene expression, suggesting a key role for condensin I in transcription during interphase. Total RNA profiles of CAP-H KO cells with or without Dox were generated by sequencing using Illumina Hiseq2000 platform.
2017-05-03 | E-GEOD-74892 | biostudies-arrayexpress
Project description:AMPK (AAK-2) and calcineurin (TAX-6) mediate longevity exclusively through post-translational modification of CRTC-1, the sole C. elegans CRTC (CREB regulated transcriptional coactivator). We performed microarrays to examine the transcriptional responses elicited by the pro-longevity: activation of AMPK, deactivation of calcineurin, and decrease of CREB (CRH-1) activity.
2010-11-20 | GSE25513 | GEO
Project description:Transplantation of differential microbiota in young germ-free donors show distinct metabolic signatures. We used microarrays to understand pathway level changes in the livers and small intestines of differential-microbiota conventionalized young recipeint mice.
2019-12-01 | GSE130026 | GEO